Expired updates not being cleaned up

Hi,
I've been trying to clean up old expired updates on my SCCM 2012 SP1 server and for whatever reason it seems that the updates files are never actually getting removed.
At first I tried the instructions at
http://blogs.technet.com/b/configmgrteam/archive/2012/04/12/software-update-content-cleanup-in-system-center-2012-configuration-manager.aspx
When I run the script they provide it appears to go thru all the updates but never actually deletes any of them. The script always seems to say found it found an existing folder and then later it says that that it is excluding the same folder because
it is active.
Then I read that SP1 for SCCM 2012 is actually supposed to do the clean up process automatically.  But in this case do I need to do anything like expire the updates manually or does SCCM now do that?  How can I see what is preventing either
the manual script or the automatic clean up process from actually removing the unneeded files and folders?
And does anything need to be done with superseded updates as well?
Also I've always thought that when you SCCM 2012 to do your updates that you should never go to the WSUS console and do anything but I read
http://blog.coretech.dk/kea/house-of-cardsthe-configmgr-software-update-point-and-wsus/ and he is going the WSUS console and doing a clean up there as well.
Thanks in advance,
Nick

Hi Xin,
In the wsyncmgr.log file I see lots of log entries like this:
Skipped update 2d8121b4-ba5c-4492-ba6e-1c70e9382406 - Update for Windows Vista (KB2998527) because it is up to date.  $$<SMS_WSUS_SYNC_MANAGER><10-31-2014 01:50:02.777+420><thread=4172 (0x104C)>
Skipped update 24d18083-0417-4273-9a5e-1fc3cd37f1d4 - Update for Windows Embedded Standard 7 for x64-based Systems (KB2998527) because it is up to date.  $$<SMS_WSUS_SYNC_MANAGER><10-31-2014 01:50:02.791+420><thread=4172 (0x104C)>
Skipped update 954f2ad2-369e-469e-97a0-3efd0a831111 - Update for Windows 8.1 (KB2998527) because it is up to date.  $$<SMS_WSUS_SYNC_MANAGER><10-31-2014 01:50:02.805+420><thread=4172 (0x104C)>
Skipped update f81d2820-721a-431c-a262-4878a42f0115 - Update for Windows Vista for x64-based Systems (KB2998527) because it is up to date.  $$<SMS_WSUS_SYNC_MANAGER><10-31-2014 01:50:02.822+420><thread=4172 (0x104C)>
Skipped update 7c82171f-025c-46af-849c-63764ba44382 - Update for Windows Server 2008 x64 Edition (KB2998527) because it is up to date.  $$<SMS_WSUS_SYNC_MANAGER><10-31-2014 01:50:02.836+420><thread=4172 (0x104C)>
Skipped update 36c29163-b78a-410f-8bd0-7370b35a24f1 - Update for Windows Server 2012 (KB2998527) because it is up to date.  $$<SMS_WSUS_SYNC_MANAGER><10-31-2014 01:50:02.850+420><thread=4172 (0x104C)>
Skipped update 6146260e-5c34-4483-962d-834250d84c79 - Update for Windows 7 (KB2998527) because it is up to date.  $$<SMS_WSUS_SYNC_MANAGER><10-31-2014 01:50:02.864+420><thread=4172 (0x104C)>
Skipped update e6e7f357-7011-4bfd-8b14-8be61e43fa51 - Update for Windows Server 2003 (KB2998527) because it is up to date.  $$<SMS_WSUS_SYNC_MANAGER><10-31-2014 01:50:02.877+420><thread=4172 (0x104C)>
Skipped update 2ed5e49f-3295-4b89-8a0b-9a38c0027d6d - Update for Windows Server 2008 R2 for Itanium-based Systems (KB2998527) because it is up to date.  $$<SMS_WSUS_SYNC_MANAGER><10-31-2014 01:50:02.890+420><thread=4172 (0x104C)>
Skipped update 62778a2a-11d8-4cb1-9970-9c3f45202d04 - Update for Windows Server 2008 R2 x64 Edition (KB2998527) because it is up to date.  $$<SMS_WSUS_SYNC_MANAGER><10-31-2014 01:50:02.905+420><thread=4172 (0x104C)>
And I also see the following entries:
Sync time: 0d00h41m29s  $$<SMS_WSUS_SYNC_MANAGER><10-30-2014 01:51:51.388+420><thread=3440 (0xD70)>
Wakeup by SCF change  $$<SMS_WSUS_SYNC_MANAGER><10-30-2014 02:05:42.535+420><thread=3440 (0xD70)>
Wakeup for a polling cycle  $$<SMS_WSUS_SYNC_MANAGER><10-30-2014 03:05:49.050+420><thread=3440 (0xD70)>
Deleting old expired updates...  $$<SMS_WSUS_SYNC_MANAGER><10-30-2014 03:05:49.130+420><thread=3440 (0xD70)>
Deleted 17 expired updates  $$<SMS_WSUS_SYNC_MANAGER><10-30-2014 03:05:57.067+420><thread=3440 (0xD70)>
Deleted 134 expired updates  $$<SMS_WSUS_SYNC_MANAGER><10-30-2014 03:06:06.487+420><thread=3440 (0xD70)>
Deleted 168 expired updates  $$<SMS_WSUS_SYNC_MANAGER><10-30-2014 03:06:07.595+420><thread=3440 (0xD70)>
Deleted 168 expired updates total  $$<SMS_WSUS_SYNC_MANAGER><10-30-2014 03:06:07.651+420><thread=3440 (0xD70)>
Deleted 10 orphaned content folders in package P0100005 (Endpoint Protection Definition Updates)  $$<SMS_WSUS_SYNC_MANAGER><10-30-2014 03:06:07.875+420><thread=3440 (0xD70)>
Deleted 5 orphaned content folders in package P0100007 (Automatic Deployment Rule for Exchange Servers)  $$<SMS_WSUS_SYNC_MANAGER><10-30-2014 03:06:07.953+420><thread=3440 (0xD70)>
Thread terminated by service request.  $$<SMS_WSUS_SYNC_MANAGER><10-30-2014 03:06:51.039+420><thread=3440 (0xD70)>
So it seems like it might be skipping updates?  And then it says it deleted 168 expired updates for example?
But if I look at the drive where all the update packages are stored it hasn't changed size.

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